Come hear Christina Azodi

“Uncovering the cis-regulatory code of plant response to combined abiotic stress using multi-dimensional data integration and machine learning”

Christina B. Azodi¹, Sahra Uygun¹, Ronan O’Malley² & Shin-Han Shiu¹

¹ Department of Plant Biology, Michigan State University, Lansing MI 48910, USA

² Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA

Plants acclimate to an environmental stress using highly tailored response pathways. When multiple stresses occur at once, acclimation may require conflicting or entirely different responses compared to the responses to each stress alone. Previous work has shown that conflicting and novel responses are common, with >60% of genes responding to combined stress antagonistically or synergistically compared to their response to the stresses individually. While multiple combined stress studies have observed these non-additive responses, the regulatory bases for these responses are still largely unknown. In this study, we identified 197 putative cis-regulatory elements (pCREs) associated with antagonistic and synergistic responses to combined drought and heat stress in Arabidopsis thaliana. These pCREs perform better at predicting a gene’s response pattern than not only random expectation, but also known transcription factor (TF) binding motifs and sites. To identify which of these pCREs are most likely to be involved in regulation, additional criteria such as chromatin accessibility, histone marks, sequence conservation, and location and distribution in the promoter were considered. Using these criteria we pared down our list to 31 high confidence pCREs. Of these, 48% share significant sequence similarity with known TF binding motifs, including TFs from the bZIP, HSF, and bHLH TF families. The remaining 52% could represent novel TF binding motifs. A subset of these high confidence pCREs is being experimentally verified. These results support the hypothesis that combinations of stresses elicit regulatory mechanisms not induced by the stresses individually. This contribution to our understanding of how plants regulate their response to more complex environmental stresses is an important step as we work toward improving crop resilience in the face of a changing climate.